truvari/Singularity.def at develop · ACEnglish/truvari · GitHub

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Bootstrap: docker
From: ubuntu:20.04
Stage: spython-base

%files
. /opt/truvari-source
%post


apt-get -qq update \
  && DEBIAN_FRONTEND=noninteractive apt-get install -yq \
  bcftools \
  curl \
  python3-dev \
  python3-pip \
  samtools \
  tabix \
  vcftools \
  wget \
  && \
  rm -rf /var/lib/apt/lists/*

cd /opt/truvari-source

wget https://mafft.cbrc.jp/alignment/software/mafft_7.505-1_amd64.deb \
    && dpkg -i mafft_7.505-1_amd64.deb && rm mafft_7.505-1_amd64.deb

python3 -m pip install --upgrade pip && \
    python3 -m pip install setproctitle pylint anybadge coverage && \
    python3 -m pip install --upgrade setuptools && \
    python3 -m pip install ./


mkdir /data
cd /data

%runscript
cd /data
exec truvari "$@"
%startscript
cd /data
exec truvari "$@"